Methods for selecting microbes from a diverse genetically modified library to detect and optimize the production of metabolites

A method of selecting a subset of microbes for the production of a metabolite comprising

• placing a population of microbes in an environment of a toxin, wherein the toxin is external to the population of microbes,
• wherein the population of microbes has been genetically modified to include exogenous DNA encoding for an antidote gene to the toxin,
• wherein the population of microbes has been genetically modified to include exogenous DNA encoding a sensor biomolecule which when expressed regulates expression of the antidote gene by the microbes through a cognate nucleic acid sequence located 5′ to the DNA encoding the antidote gene, wherein the sensor biomolecule is a transcription factor, riboswitch, two-component signaling protein or a nuclear hormone receptor,
• wherein the population of microbes has been genetically modified to include exogenous DNA encoding genes to produce a metabolite binding partner of the sensor, which when produced binds to the sensor to induce expression of the antidote gene in a manner dependent on the concentration of the produced metabolite, and
• selecting a subset of microbes that produce sufficient metabolite to prevent microbe death,
• wherein the sensor biomolecule and its corresponding metabolite binding partner is selected from the group consisting of cdaR and glucaric acid, ttgR and naringennin, btuB riboswitch and cobalamin, mphR and macrolides, benM and muconic acid, alkS and medium chain n-alkanes, xylR and xylose, araC and arabinose, gntR and Gluconate, galS and galactose, trpR and tryptophan, qacR and berberine, rmrR and Phytoalexin, cymR and cumate, melR and melibiose, rafR and raffinose, nahR and salicylate, nocR and nopaline, clcR and Chlorobenzoate, varR and virginiamycin, rhaR and rhamnose, PhoR and phosphate, MalK and malate, GlnK and glutamine, retinoic acid receptor and retinoic acid, estrogen receptor and estrogen, and ecdysone receptor and ecdysone,
• wherein the toxin and antidote pair is selected from the group consisting of SDS:tolC, colicin:tolC (negative selection), kanamycin:kanamycin nucleotidyltransferase, chloramphenicol:chloramphenicol acyl transferase, ampicillin:beta lactamase, tetracycline:tetracycline efflux pump tetA, nickel chloride:tetracycline efflux pump tetA (negative selection), and 5-fluoroorotic acid:URA3 (negative selection).